Deriving phylogenetic trees from the similarity analysis of metabolic pathways

Motivation: Comparative analysis of metabolic pathways in different genomes can give insights into the understanding of evolutionary and organizational relationships among species. This type of analysis allows one to measure the evolution of complete processes (with different functional roles) rathe...

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Bibliographic Details
Published in:Bioinformatics 2003, Vol.19 (suppl-1), p.i138-i146
Main Authors: Heymans, Maureen, Singh, Ambuj K.
Format: Article
Language:English
Subjects:
Algorithms
Carbohydrate Metabolism
Carbohydrates - genetics
Citric Acid Cycle - physiology
Computer Simulation
Gene Expression Profiling - methods
Gene Expression Regulation - physiology
Glycolysis - physiology
Metabolism - physiology
Models, Biological
Multienzyme Complexes - genetics
Multienzyme Complexes - metabolism
Pattern Recognition, Automated
Phylogeny
Signal Transduction - physiology
Software
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Summary:Motivation: Comparative analysis of metabolic pathways in different genomes can give insights into the understanding of evolutionary and organizational relationships among species. This type of analysis allows one to measure the evolution of complete processes (with different functional roles) rather than the individual elements of a conventional analysis. We present a new technique for the phylogenetic analysis of metabolic pathways based on the topology of the underlying graphs. A distance measure between graphs is defined using the similarity between nodes of the graphs and the structural relationship between them. This distance measure is applied to the enzyme-enzyme relational graphs derived from metabolic pathways. Using this approach, pathways and group of pathways of different organisms are compared to each other and the resulting distance matrix is used to obtain a phylogenetic tree. Results: We apply the method to the Citric Acid Cycle and the Glycolysis pathways of different groups of organisms, as well as to the Carbohydrate metabolic networks. Phylogenetic trees obtained from the experiments were close to existing phylogenies and revealed interesting relationships among organisms. Availability: Software available upon request from the authors. Supplementary information: The technical report is available at http://www.cs.ucsb.edu/~maureen/TR200233.pdf Contact: ambuj@cs.ucsb.edu Keywords: phylogenetic trees, metabolic pathways, graph comparison * To whom correspondence should be addressed.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btg1018